Mesozooplankton grazing minimally impacts phytoplankton abundance during spring in the western North Atlantic
The impacts of grazing by meso- and microzooplankton on phytoplankton primary production (PP) was investigated in the surface layer of the western North Atlantic during spring. Shipboard experiments were performed on a latitudinal transect at three stations that differed in mixed layer depth, temperature, and mesozooplankton taxonomic composition. The mesozooplankton community was numerically dominated by Calanus finmarchicus at the northern and central station, with Calanus hyperboreus also present at the northern station. The southern station was >10 °C warmer than the other stations and had the most diverse mesozooplankton assemblage, dominated by small copepods including Paracalanus spp. Microzooplankton grazing was detected only at the northern station, where it removed 97% of PP. Estimated clearance rates by C. hyperboreus and C. finmarchicus suggested that at in-situ abundance these mesozooplankton were not likely to have a major impact on phytoplankton abundance, unless locally aggregated. Although mesozooplankton grazing impact on total phytoplankton was minimal, these grazers completely removed the numerically scarce > 10 µm particles, altering the particle-size spectrum. At the southern station, grazing by the whole mesozooplankton assemblage resulted in a removal of 14% of PP, and its effect on net phytoplankton growth rate was similar irrespective of ambient light. In contrast, reduction in light availability had an approximately 3-fold greater impact on net phytoplankton growth rate than mesozooplankton grazing pressure. The low mesozooplankton grazing impact across stations suggests limited mesozooplankton-mediated vertical export of phytoplankton production. The constraints provided here on trophic transfer, as well as quantitative estimates of the relative contribution of light and grazer controls of PP and of grazer-induced shifts in particle size spectra, illuminate food web dynamics and aid in parameterizing modeling-frameworks assessing global elemental fluxes and carbon export.
Morison et al. (2020) Mesozooplankton grazing minimally impacts phytoplankton abundance during spring in the western North Atlantic. PeerJ 8:e9430 https://doi.org/10.7717/peerj.9430
The switch from one substance-of-abuse to another: illicit drug substitution behaviors in a sample of high-risk drug users
Background Substitution can be defined as the consciously motivated choice to use one drug, either licit or illicit, instead of another, due to perceptions of cost, availability, safety, legality, substance characteristics, and substance attributions. Substitution represents a potential risk to drug users, mainly when substitutes are of higher potency and toxicity. This study offers a basic conceptualization of illicit substitution behavior and describes substitution patterns among users of two highly prevalent drugs of abuse—heroin and cannabis. Methods Here, 592 high-risk drug users undergoing pharmacological and psycho-social treatment were interviewed. Patients were asked questions about current drug use, lifetime substitution, and substitution patterns. Descriptive statistics, chi-square tests of independence, and multinomial logistic regressions were used to identify and test correlates of substitution patterns for heroin and cannabis. Results Of the 592 drug users interviewed, 448 subjects (75.7%) reported having substituted their preferred drug for another illicit substance. Interviews yielded a total of 275 substitution events reported by users of cannabis, and 351 substitution events reported by users of heroin. The most frequently reported substitution substances for responders who preferred heroin were illicit non-prescribed “street” methadone (35.9%), followed by oral and transdermal prescription opioids (17.7%). For responders who preferred cannabis, substitution for synthetic cannabinoid receptor agonists (33.5%) followed by alcohol (16.0%) were the most commonly reported. Age at onset–of–use (p < 0.005), population group (p = 0.008), and attending treatment for the first time (p = 0.026) were significantly associated with reported lifetime substitution. Past-year use of stimulants, heroin, hallucinogens, methylenedioxymethamphetamine (MDMA), and novel psychoactive substances were—at the 95% confidence level—also significantly associated with reported lifetime substitution. In multivariate analysis, the odds for methadone substitution among heroin users were significantly affected by age at onset-of-use, type of treatment center, and education. Odds for substitution for synthetic cannabinoid receptor agonists among cannabis users were significantly affected by age, population group, type of treatment center, and education. Conclusion Self-substitution behavior should be considered by clinicians and policymakers as a common practice among most drugusers. Substitution for street methadone provides evidence for the ongoing diversion of this substance from Opioid Maintenance Treatment Centers, while the prominence of substitution of synthetic cannabinoids among dual-diagnosis patients should be regarded as an ongoing risk to patients that needs to be addressed by clinicians. Analysis of additional substitution patterns should provide further valuable insights into the behavior of drugusers.
Shapira et al. (2020) The switch from one substance-of-abuse to another: illicit drug substitution behaviors in a sample of high-risk drug users. PeerJ 8:e9461 https://doi.org/10.7717/peerj.9461
Mechanisms behind bottom-up effects: eutrophication increases fecundity by shortening the interspawning interval in stickleback
Anthropogenic eutrophication is altering aquatic environments by promoting primary production. This influences the population dynamics of consumers through bottom-up effects, but the underlying mechanisms and pathways are not always clear. To evaluate and mitigate effects of eutrophication on ecological communities, more research is needed on the underlying factors. Here we show that anthropogenic eutrophication increases population fecundity in the threespine stickleback (Gasterosteus aculeatus) by increasing the number of times females reproduce—lifetime fecundity—rather than instantaneous fecundity. When we exposed females to nutrient-enriched waters with enhanced algal growth, their interspawning interval shortened but the size of their egg clutches, or the size of their eggs, did not change. The shortening of the interspawning interval was probably caused by higher food intake, as algae growth promotes the growth of preferred prey populations. Enhanced female lifetime fecundity could increase offspring production and, hence, influence population dynamics. In support of this, earlier studies show that more offspring are emerging in habitats with denser algae growth. Thus, our results stress the importance of considering lifetime fecundity, in addition to instantaneous fecundity, when investigating the impact of human-induced eutrophication on population processes. At a broader level, our results highlight the importance of following individuals over longer time spans when evaluating the pathways and processes through which environmental changes influence individual fitness and population processes.
Saarinen et al. (2020) Mechanisms behind bottom-up effects: eutrophication increases fecundity by shortening the interspawning interval in stickleback. PeerJ 8:e9521 https://doi.org/10.7717/peerj.9521
Genome-wide identification and expression profiles of ERF subfamily transcription factors in Zea mays
The Ethylene-Response Factor (ERF) subfamily transcription factors (TFs) belong to the APETALA2/Ethylene-Responsive Factor (AP2/ERF) superfamily and play a vital role in plant growth and development. However, identification and analysis of the ERF subfamily genes in maize have not yet been performed at genome-wide level. In this study, a total of 76 ERF subfamily TFs were identified and were found to be unevenly distributed on the maize chromosomes. These maize ERF (ZmERF) TFs were classified into six groups, namely groups B1 to B6, based on phylogenetic analysis. Synteny analysis showed that 50, 54, and 58 of the ZmERF genes were orthologous to those in rice, Brachypodium, and Sorghum, respectively. Cis-element analysis showed that elements related to plant growth and development, hormones, and abiotic stress were identified in the promoter region of ZmERF genes. Expression profiles suggested that ZmERF genes might participate in plant development and in response to salinity and drought stresses. Our findings lay a foundation and provide clues for understanding the biological functions of ERF TFs in maize.
Hao et al. (2020) Genome-wide identification and expression profiles of ERF subfamily transcription factors in Zea mays. PeerJ 8:e9551 https://doi.org/10.7717/peerj.9551
Understanding genomic diversity, pan-genome, and evolution of SARS-CoV-2
Coronovirus disease 2019 (COVID-19) infection, which originated from Wuhan, China, has seized the whole world in its grasp and created a huge pandemic situation before humanity. Since December 2019, genomes of numerous isolates have been sequenced and analyzed for testing confirmation, epidemiology, and evolutionary studies. In the first half of this article, we provide a detailed review of the history and origin of COVID-19, followed by the taxonomy, nomenclature and genome organization of its causative agent Severe Acute Respiratory Syndrome-related Coronavirus-2 (SARS-CoV-2). In the latter half, we analyze subgenus Sarbecovirus (167 SARS-CoV-2, 312 SARS-CoV, and 5 Pangolin CoV) genomes to understand their diversity, origin, and evolution, along with pan-genome analysis of genus Betacoronavirus members. Whole-genome sequence-based phylogeny of subgenus Sarbecovirus genomes reasserted the fact that SARS-CoV-2 strains evolved from their common ancestors putatively residing in bat or pangolin hosts. We predicted a few country-specific patterns of relatedness and identified mutational hotspots with high, medium and low probability based on genome alignment of 167 SARS-CoV-2 strains. A total of 100-nucleotide segment-based homology studies revealed that the majority of the SARS-CoV-2 genome segments are close to Bat CoV, followed by some to Pangolin CoV, and some are unique ones. Open pan-genome of genus Betacoronavirus members indicates the diversity contributed by the novel viruses emerging in this group. Overall, the exploration of the diversity of these isolates, mutational hotspots and pan-genome will shed light on the evolution and pathogenicity of SARS-CoV-2 and help in developing putative methods of diagnosis and treatment.
Parlikar et al. (2020) Understanding genomic diversity, pan-genome, and evolution of SARS-CoV-2. PeerJ 8:e9576 https://doi.org/10.7717/peerj.9576
Assessment of biomass potentials of microalgal communities in open pond raceways using mass cultivation
Metagenome studies have provided us with insights into the complex interactions of microorganisms with their environments and hosts. Few studies have focused on microalgae-associated metagenomes, and no study has addressed aquatic microalgae and their bacterial communities in open pond raceways (OPRs). This study explored the possibility of using microalgal biomasses from OPRs for biodiesel and biofertilizer production. The fatty acid profiles of the biomasses and the physical and chemical properties of derived fuels were evaluated. In addition, the phenotype-based environmental adaptation ability of soybean plants was assessed. The growth rate, biomass, and lipid productivity of microalgae were also examined during mass cultivation from April to November 2017. Metagenomics analysis using MiSeq identified ∼127 eukaryotic phylotypes following mass cultivation with (OPR 1) or without (OPR 3) a semitransparent film. Of these, ∼80 phylotypes were found in both OPRs, while 23 and 24 phylotypes were identified in OPRs 1 and 3, respectively. The phylotypes belonged to various genera, such as Desmodesmus, Pseudopediastrum, Tetradesmus, and Chlorella, of which, the dominant microalgal species was Desmodesmus sp. On average, OPRs 1 and 3 produced ∼8.6 and 9.9 g m−2 d−1 (0.307 and 0.309 DW L−1) of total biomass, respectively, of which 14.0 and 13.3 wt% respectively, was lipid content. Fatty acid profiling revealed that total saturated fatty acids (mainly C16:0) of biodiesel obtained from the microalgal biomasses in OPRs 1 and 3 were 34.93% and 32.85%, respectively; total monounsaturated fatty acids (C16:1 and C18:1) were 32.40% and 31.64%, respectively; and polyunsaturated fatty acids (including C18:3) were 32.68% and 35.50%, respectively. Fuel properties determined by empirical equations were within the limits of biodiesel standards ASTM D6751 and EN 14214. Culture solutions with or without microalgal biomasses enhanced the environmental adaptation ability of soybean plants, increasing their seed production. Therefore, microalgal biomass produced through mass cultivation is excellent feedstock for producing high-quality biodiesel and biofertilizer.
Jo et al. (2020) Assessment of biomass potentials of microalgal communities in open pond raceways using mass cultivation. PeerJ 8:e9418 https://doi.org/10.7717/peerj.9418
Subcellular compartmentalization of the plant antioxidant system: an integrated overview
The antioxidant system (AOS) maintains the optimal concentration of reactive oxygen species (ROS) in a cell and protects it against oxidative stress. In plants, the AOS consists of seven main classes of antioxidant enzymes, low-molecular antioxidants (e.g., ascorbate, glutathione, and their oxidized forms) and thioredoxin/glutaredoxin systems which can serve as reducing agents for antioxidant enzymes. The number of genes encoding AOS enzymes varies between classes, and same class enzymes encoded by different gene copies may have different subcellular localizations, functional loads and modes of evolution. These facts hereafter reinforce the complex nature of AOS regulation and functioning. Further studies can describe new trends in the behavior and functioning of systems components, and provide new fundamental knowledge about systems regulation. The system is revealed to have a lot of interactions and interplay pathways between its components at the subcellular level (antioxidants, enzymes, ROS level, and hormonal and transcriptional regulation). These facts should be taken into account in further studies during the AOS modeling by describing the main pathways of generating and utilizing ROS, as well as the associated signaling processes and regulation of the system on cellular and organelle levels, which is a complicated and ambitious task. Another objective for studying the phenomenon of the AOS is related to the influence of cell dynamics and circadian rhythms on it. Therefore, the AOS requires an integrated and multi-level approach to study. We focused this review on the existing scientific background and experimental data used for the systems biology research of the plant AOS.
Bobrovskikh et al. (2020) Subcellular compartmentalization of the plant antioxidant system: an integrated overview. PeerJ 8:e9451 https://doi.org/10.7717/peerj.9451
The chemotactic swimming behavior of bird schistosome miracidia in the presence of compatible and incompatible snail hosts
No effective method has yet been developed to prevent the threat posed by the emerging disease—cercarial dermatitis (swimmer’s itch), caused by infective cercariae of bird schistosomes (Digenea: Schistosomatidae). In our previous studies, the New Zealand mud snail—Potamopyrgus antipodarum (Gray, 1853; Gastropoda, Tateidae)—was used as a barrier between the miracidia of Trichobilharzia regenti and the target snails Radix balthica. Since the presence of non-indigenous snails reduced the parasite prevalence under laboratory conditions, we posed three new research questions: (1) Do bird schistosomes show totally perfect efficacy for chemotactic swimming behavior? (2) Do the larvae respond to substances emitted by incompatible snail species? (3) Do the excretory-secretory products of incompatible snail species interfere with the search for a compatible snail host? The experiments were carried out in choice-chambers for the miracidia of T. regenti and T. szidati. The arms of the chambers, depending on the variant, were filled with water conditioned by P. antipodarum, water conditioned by lymnaeid hosts, and dechlorinated tap water. Miracidia of both bird schistosome species chose more frequently the water conditioned by snails—including the water conditioned by the incompatible lymnaeid host and the alien species, P. antipodarum. However, species-specific differences were noticed in the behavior of miracidia. T. regenti remained more often inside the base arm rather than in the arm filled with water conditioned by P. antipodarum or the control arm. T. szidati, however, usually left the base arm and moved to the arm filled with water conditioned by P. antipodarum. In conclusion, the non-host snail excretory-secretory products may interfere with the snail host-finding behavior of bird schistosome miracidia and therefore they may reduce the risk of swimmer’s itch.
Marszewska et al. (2020) The chemotactic swimming behavior of bird schistosome miracidia in the presence of compatible and incompatible snail hosts. PeerJ 8:e9487 https://doi.org/10.7717/peerj.9487
Review of the genus Loimia Malmgren, 1866 (Annelida, Terebellidae) from China seas with recognition of two new species based on integrative taxonomy
Specimens of the genus Loimia (Annelida, Terebellidae) deposited in the Marine Biological Museum of the Chinese Academy of Sciences (MBMCAS) together with materials newly collected from China seas were examined. Based on morphological comparisons and molecular analysis, some specimens collected from the coasts of Shandong province and Guangxi province were confirmed as two new Loimia species respectively (Loimia borealis sp. n. and Loimia macrobranchia sp. n.). Morphologically, L. borealis sp. n. is distinguished from previously known species of this genus by having seven equal sized ventral shields, with length five times the width; this species was retrieved as sister to the clades of Loimia arborea Moore, 1903 and Loimia bandera Hutchings, 1990 in the phylogenetic tree, which was reconstructed based on mitochondrial COI gene. Loimia macrobranchia sp. n. differs from congeners by the large size of its first pair of branchiae with a thick main stem and about 18 dendritic branches arranged in two levels. A key to identifying Loimia species found in Chinese seas is given.
Wang et al. (2020) Review of the genus Loimia Malmgren, 1866 (Annelida, Terebellidae) from China seas with recognition of two new species based on integrative taxonomy. PeerJ 8:e9491 https://doi.org/10.7717/peerj.9491
Light dependent courtship behavior in Drosophila simulans and D. melanogaster
Differences in courtship signals and perception are well-known among Drosophila species. One such described difference is the dependency on light, and thus presumably vision, for copulation success. Many studies have described a difference in light-dependent copulation success between D. melanogaster and D. simulans, identifying D. simulans as a light-dependent species, and D. melanogaster as a light-independent one. However, many of these studies use assays of varying design and few strains to represent the entire species. Here, we attempt to better characterize this purported difference using 11 strains of each species, paired by collection location, in behavioral assays conducted at two different exposure times. We show that, while there is a species-wide difference in magnitude of light-dependent copulation success, D. melanogaster copulation success is, on average, still impaired in the dark at both exposure times we measured. Additionally, there is significant variation in strain-specific ability to copulate in the dark in both species across two different exposure times. We find that this variation correlates strongly with longitude in D. melanogaster, but not in D. simulans. We hypothesize that differences in species history and demography may explain behavioral variation. Finally, we use courtship assays to show that light-dependent copulation success in one D. simulans strain is driven in part by both males and females. We discuss potential differences in courtship signals and/or signal importance between these species and potential for further comparative studies for functional characterization.
Shahandeh et al. (2020) Light dependent courtship behavior in Drosophila simulans and D. melanogaster. PeerJ 8:e9499 https://doi.org/10.7717/peerj.9499